Locus 7714

Sequence ID	3L_DroMel_CAF1
Location	20,613,831 – 20,614,056
Length	225
Max. P	0.954982

overview

Window 5

Location	20,613,831 – 20,613,945
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.56
Mean single sequence MFE	-25.20
Consensus MFE	-22.98
Energy contribution	-22.82
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.59
Structure conservation index	0.91
SVM decision value	1.42
SVM RNA-class probability	0.952304
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613831 114 + 23771897
AAAAAUAACUUUGACAAUAU------GCCAAAGGGGGACACCGGCUUAAGGCAAUUAAUUUCGAUAAUAAUUGUUCAAUGUGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUA
..........(((((....(------((((((((....).(((.(....((((((((..........))))))))....))))..))))))))...(((.....))))))))........ ( -24.40)
>DroSec_CAF1 58604 114 + 1
AAAAAUAACUUUGACAAUAU------GCCAAAGGGGGACACCGGCUUAAGGCAAUUAAUUUCGAUAAUAAUUGUUCAAUGUGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUA
..........(((((....(------((((((((....).(((.(....((((((((..........))))))))....))))..))))))))...(((.....))))))))........ ( -24.40)
>DroAna_CAF1 80605 120 + 1
AAAAAUAACUUUGACAAUAUCAGUAAGCCGAAGGGGGACAUCGGCUUAAGGCAAUUAAUUUCUAUAAUAAUUGUUCAAUGUAGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUA
..........(((((....((..((((((((..(....).)))))))).((((((((..........)))))))).......))((((..(.........)..)))))))))........ ( -28.40)
>DroSim_CAF1 53506 114 + 1
AAAAAUAACUUUGACAAUAU------GCCAAAGGGGGACACCGGCUUAAGGCAAUUAAUUUCGAUAAUAAUUGUUCAAUGUGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUA
..........(((((....(------((((((((....).(((.(....((((((((..........))))))))....))))..))))))))...(((.....))))))))........ ( -24.40)
>DroEre_CAF1 51144 114 + 1
AAAAAUAACUUUGACAAUAU------GCCAAAGGGGGACACCGGCUUAAGGCAAUUAAUUUCGAUAAUAAUUGUUCAAUGUGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUA
..........(((((....(------((((((((....).(((.(....((((((((..........))))))))....))))..))))))))...(((.....))))))))........ ( -24.40)
>consensus
AAAAAUAACUUUGACAAUAU______GCCAAAGGGGGACACCGGCUUAAGGCAAUUAAUUUCGAUAAUAAUUGUUCAAUGUGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUA
..........(((((...........((((((((....)..(.((....((((((((..........))))))))....)).)..)))))))....(((.....))))))))........ (-22.98 = -22.82 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	20,613,905 – 20,614,016
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.67
Mean single sequence MFE	-25.24
Consensus MFE	-20.16
Energy contribution	-21.36
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.80
SVM decision value	0.25
SVM RNA-class probability	0.653763
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613905 111 + 23771897
UGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUAAUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUA---CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCA
.(..((((..(.........)..))))..)...............(((((((.....((((((.....((((((.------...---..))))))....)).)))).....))))))).. ( -26.50)
>DroSec_CAF1 58678 111 + 1
UGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUAAUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUA---CCUAUUUACGUGCACGGGUAUAUAUGGGGAGCA
.(..((((..(.........)..))))..)...............((((((..(........)........((((------(((---(((............)))))))))))))))).. ( -24.50)
>DroAna_CAF1 80685 106 + 1
UAGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUAAUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUAGCCUCUAGAUACGUG--------UAUAUGGGGAGCA
..((((((..(.........)..)))).))...............(((((((.(........).....((((((.------.((.........))..))--------))))))))))).. ( -18.50)
>DroSim_CAF1 53580 111 + 1
UGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUAAUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUA---CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCA
.(..((((..(.........)..))))..)...............(((((((.....((((((.....((((((.------...---..))))))....)).)))).....))))))).. ( -26.50)
>DroEre_CAF1 51218 117 + 1
UGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUAAUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAUACACGUAUA---CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCA
.(..((((..(.........)..))))..)...............(((((((.....((((.(....)........((((((((---....))))))))...)))).....))))))).. ( -30.20)
>consensus
UGGAGCUUUGGCAAAAGUUACUGAAGCGUCGACAAUAAUAAUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU______AUA___CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCA
..((((((..(.........)..)))).))...............(((((((.....((((....((.((((((...............)))))).))....)))).....))))))).. (-20.16 = -21.36 +   1.20)

alignment

secondary structure

dotplot

Window 7

Location	20,613,945 – 20,614,056
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.02
Mean single sequence MFE	-24.32
Consensus MFE	-19.72
Energy contribution	-20.92
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.81
SVM decision value	1.45
SVM RNA-class probability	0.954982
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613945 111 + 23771897
AUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUA---CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCAAGUCAUUAACGAGCUCUCGAACAGCUCUCGAACAAUGAAC
.....(((((((.....((((((.....((((((.------...---..))))))....)).)))).....)))))))....(((((...(((((.......)))))......))))).. ( -25.50)
>DroSec_CAF1 58718 111 + 1
AUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUA---CCUAUUUACGUGCACGGGUAUAUAUGGGGAGCAAGUCAUUAACGAGCUCUCGAACAGCUCUCGAACAAUGAAC
.....((((((..(........)........((((------(((---(((............))))))))))))))))....(((((...(((((.......)))))......))))).. ( -23.50)
>DroAna_CAF1 80725 106 + 1
AUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUAGCCUCUAGAUACGUG--------UAUAUGGGGAGCAAGUCAUUAACGAGCUCUCGAACAGCUCUCGAACAAUGAAC
.....(((((((.(........).....((((((.------.((.........))..))--------)))))))))))....(((((...(((((.......)))))......))))).. ( -17.90)
>DroSim_CAF1 53620 111 + 1
AUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU------AUA---CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCAAGUCAUUAACGAGCUCUCGAACAGCUCUCGAACAAUGAAC
.....(((((((.....((((((.....((((((.------...---..))))))....)).)))).....)))))))....(((((...(((((.......)))))......))))).. ( -25.50)
>DroEre_CAF1 51258 117 + 1
AUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAUACACGUAUA---CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCAAGUCAUUAACGAGCUCUCGAACAGCUCUCGAACAAUGAAC
.....(((((((.....((((.(....)........((((((((---....))))))))...)))).....)))))))....(((((...(((((.......)))))......))))).. ( -29.20)
>consensus
AUAACUUCCCCAACUUAACCCUGAAAUCUAUAUAU______AUA___CCUAUAUACGUGCACGGGUAUAUAUGGGGAGCAAGUCAUUAACGAGCUCUCGAACAGCUCUCGAACAAUGAAC
.....(((((((.....((((....((.((((((...............)))))).))....)))).....)))))))....(((((...(((((.......)))))......))))).. (-19.72 = -20.92 +   1.20)

alignment

secondary structure

dotplot

Window 8

Location	20,613,945 – 20,614,056
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.02
Mean single sequence MFE	-32.40
Consensus MFE	-25.70
Energy contribution	-26.90
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.79
SVM decision value	1.11
SVM RNA-class probability	0.917088
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613945 111 - 23771897
GUUCAUUGUUCGAGAGCUGUUCGAGAGCUCGUUAAUGACUUGCUCCCCAUAUAUACCCGUGCACGUAUAUAGG---UAU------AUAUAUAGAUUUCAGGGUUAAGUUGGGGAAGUUAU
..((((((..((((..((.....))..)))).))))))...((((((((.....((((......(((((((..---..)------))))))........)))).....))))).)))... ( -31.94)
>DroSec_CAF1 58718 111 - 1
GUUCAUUGUUCGAGAGCUGUUCGAGAGCUCGUUAAUGACUUGCUCCCCAUAUAUACCCGUGCACGUAAAUAGG---UAU------AUAUAUAGAUUUCAGGGUUAAGUUGGGGAAGUUAU
..((((((..((((..((.....))..)))).))))))...((((((((((((((((..(........)..))---)))------))))...(((((.......))))))))).)))... ( -29.40)
>DroAna_CAF1 80725 106 - 1
GUUCAUUGUUCGAGAGCUGUUCGAGAGCUCGUUAAUGACUUGCUCCCCAUAUA--------CACGUAUCUAGAGGCUAU------AUAUAUAGAUUUCAGGGUUAAGUUGGGGAAGUUAU
..((((((..((((..((.....))..)))).))))))...((((((((....--------.((..((((.((((((((------....)))).)))).))))...))))))).)))... ( -27.60)
>DroSim_CAF1 53620 111 - 1
GUUCAUUGUUCGAGAGCUGUUCGAGAGCUCGUUAAUGACUUGCUCCCCAUAUAUACCCGUGCACGUAUAUAGG---UAU------AUAUAUAGAUUUCAGGGUUAAGUUGGGGAAGUUAU
..((((((..((((..((.....))..)))).))))))...((((((((.....((((......(((((((..---..)------))))))........)))).....))))).)))... ( -31.94)
>DroEre_CAF1 51258 117 - 1
GUUCAUUGUUCGAGAGCUGUUCGAGAGCUCGUUAAUGACUUGCUCCCCAUAUAUACCCGUGCACGUAUAUAGG---UAUACGUGUAUAUAUAGAUUUCAGGGUUAAGUUGGGGAAGUUAU
..((((((..((((..((.....))..)))).))))))...((((((((.....(((((((((((((((....---))))))))))).....(....).)))).....))))).)))... ( -41.10)
>consensus
GUUCAUUGUUCGAGAGCUGUUCGAGAGCUCGUUAAUGACUUGCUCCCCAUAUAUACCCGUGCACGUAUAUAGG___UAU______AUAUAUAGAUUUCAGGGUUAAGUUGGGGAAGUUAU
..((((((..((((..((.....))..)))).))))))...((((((((.....((((.......((((((...............)))))).......)))).....))))).)))... (-25.70 = -26.90 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:53 2006